MolNFT v1 · #127588 · protein
Crystal structure of human BETA1-coronavirus OC43 NL/A/2005 hemagglutinin-esterase
5N11: “Crystal structure of human BETA1-coronavirus OC43 NL/A/2005 hemagglutinin-esterase”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 8 pockets (best druggability 0.70). MolNFT v1 #127588 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5N11
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-esterase
- EC
- 3.1.1.53
- UniProt
- Q4VID6
- Ligands
- NAG, MAN, BMA
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 342 | 18% helix, 32% strand | Q4VID6 |
| B | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 348 | 16% helix, 36% strand | Q4VID6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.70 | 0.75 | 56 | empty |
| 2 | 137 | 0.60 | 0.84 | 24 | empty |
| 3 | 79 | 0.54 | 0.85 | 20 | empty |
| 4 | 92 | 0.44 | 0.80 | 22 | empty |
| 5 | 76 | 0.36 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1213 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 5N11 · Crystal structure of Human beta1-coronavirus OC43 NL/A/2005 Hemagglutinin-Esterase · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q4VID6
- Elsewhere: RCSB PDB 5N11 · PDBe 5N11 · UniProt Q4VID6
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